LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
  using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles

units		lj
atom_style	sphere
dimension	2

lattice		sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region		box block 0 60 0 60 -0.5 0.5
create_box	2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
  2 by 2 by 1 MPI processor grid
create_atoms	1 box
Created 3600 atoms
  create_atoms CPU = 0.063 seconds
change_box      all triclinic
Changing box ...
  triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)

# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms  region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms  region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds

set		type 2 mass 400
Setting atom values ...
  2 settings made for mass
set		type 1 mass 1
Setting atom values ...
  3288 settings made for mass
set     type 2 diameter 20
Setting atom values ...
  2 settings made for diameter
set     type 1 diameter 1
Setting atom values ...
  3288 settings made for diameter

velocity	all create 1.44 87287 loop geom

# multi neighbor and comm for efficiency

neighbor	1 multi/old #multi
neigh_modify	delay 0 #collection/interval 2 1 20
comm_modify     mode multi/old vel yes #reduce/multi

# colloid potential

pair_style      granular
pair_coeff      * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity

fix		1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix		2 all enforce2d
fix             3 all deform 1 xy erate 1e-3

#dump		1 all custom 1000 dump.granular id x y z radius

#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5

#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5

thermo_style	custom step temp epair etotal press vol
thermo		1000

timestep	0.005

run		50000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 21
  ghost atom cutoff = 21
  binsize = 1, bins = 85 85 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair granular, perpetual
      attributes: half, newton on, size, history
      pair build: half/size/multi/old/newton/tri
      stencil: half/multi/old/2d/tri
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes
Step Temp E_pair TotEng Press Volume 
       0         1.44            0    1.4395623   0.66837658         7200 
    1000   0.32273428            0   0.32263619   0.17174972    7859.8897 
    2000   0.12441598            0   0.12437817  0.067078155    8212.9946 
    3000  0.067389284            0  0.067368801  0.040425551    8336.7112 
    4000  0.044312733            0  0.044299264  0.028220228    8229.0658 
    5000  0.032702163            0  0.032692223  0.024302012    7931.1298 
    6000     0.025856            0  0.025848141  0.021241317    7603.5534 
    7000  0.021437473            0  0.021430957  0.019285494    7243.5757 
    8000  0.018129567            0  0.018124057  0.020738727    6877.4816 
    9000   0.01637016            0  0.016365184  0.020261904    6515.3445 
   10000   0.01500918            0  0.015004618  0.020551803    6160.4475 
   11000  0.014156553            0   0.01415225  0.021324818    5815.4665 
   12000  0.013725412            0   0.01372124  0.021159958    5483.6304 
   13000  0.013215733            0  0.013211716  0.021685624    5165.4758 
   14000  0.012398179            0  0.012394411  0.024155572    4862.8657 
   15000   0.01184269            0   0.01183909  0.028504106     4577.901 
   16000   0.01143291            0  0.011429435  0.033564204      4309.88 
   17000  0.011166204            0   0.01116281  0.040588854    4058.9972 
   18000  0.011000875            0  0.010997532  0.048998904    3825.1569 
   19000  0.010225905            0  0.010222797  0.063669588    3607.6622 
   20000 0.0091390255            0 0.0091362477  0.088165402     3408.567 
   21000 0.0077382041            0 0.0077358521   0.11770474    3227.6936 
   22000   0.00601731            0 0.0060154811   0.15261994    3064.3873 
   23000 0.0046667591            0 0.0046653407   0.19453819    2917.9782 
   24000 0.0040425749            0 0.0040413461   0.24145833    2788.3897 
   25000 0.0031933217            0 0.0031923511   0.28989713    2674.5164 
   26000 0.0021138997            0 0.0021132571   0.33598673    2574.9312 
   27000  0.001700508            0 0.0016999912   0.37665013    2487.1626 
   28000 0.0014434246            0 0.0014429859   0.41572163     2409.327 
   29000 0.00089885063            0 0.00089857742     0.453431    2340.2313 
   30000 0.00048556478            0 0.00048541719   0.49176025    2279.2155 
   31000 0.00058130972            0 0.00058113303   0.53236818    2226.2349 
   32000 0.00057749847            0 0.00057732294    0.5691506    2181.2738 
   33000 0.00044719326            0 0.00044705733   0.59696179     2142.571 
   34000 0.00060924828            0 0.0006090631   0.61735036    2107.1282 
   35000 0.00077419805            0 0.00077396273   0.63696098    2072.6008 
   36000 0.00055752003            0 0.00055735057   0.65981842    2038.8242 
   37000 0.00031402452            0 0.00031392907   0.69018949    2007.3235 
   38000 0.00034969879            0 0.0003495925   0.72155053    1980.1706 
   39000 0.00041434197            0 0.00041421603   0.74680715    1957.3838 
   40000 0.00037229243            0 0.00037217927   0.76581686    1936.8034 
   41000 0.00031028842            0 0.00031019411   0.78321059    1916.1108 
   42000 0.00026623668            0 0.00026615575   0.80267329    1894.4649 
   43000 0.00020543723            0 0.00020537479   0.82714001    1872.7672 
   44000 0.0001563321            0 0.00015628458   0.85496396    1853.0284 
   45000 0.00014981713            0 0.00014977159   0.87924842    1836.4755 
   46000 0.00015641585            0 0.00015636831   0.89896936    1822.1989 
   47000 0.00016004701            0 0.00015999837   0.91661933    1808.4606 
   48000 0.00017437702            0 0.00017432402   0.93565475    1794.1258 
   49000 0.00018645903            0 0.00018640235   0.95733183    1779.4032 
   50000 0.00018469122            0 0.00018463508   0.96446925    1765.1534 
Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms

Performance: 716540.413 tau/day, 1658.658 timesteps/s
90.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 8.7565     | 12.704     | 16.036     |  89.8 | 42.14
Neigh   | 0.4494     | 0.56436    | 0.66263    |  11.8 |  1.87
Comm    | 9.5962     | 12.989     | 17.006     |  90.8 | 43.09
Output  | 0.00088467 | 0.0011022  | 0.0015811  |   0.9 |  0.00
Modify  | 2.9732     | 3.0944     | 3.2463     |   7.0 | 10.27
Other   |            | 0.7918     |            |       |  2.63

Nlocal:        822.500 ave         859 max         785 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:        3049.75 ave        3089 max        2999 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs:        13440.5 ave       14459 max       11964 min
Histogram: 1 0 0 0 0 1 0 0 1 1

Total # of neighbors = 53762
Ave neighs/atom = 16.341033
Neighbor list builds = 348
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:30
